Living cells must constantly process information to keep track of the changing world around them and arrive at an appropriate response.

Through billions of years of trial and error, evolution has arrived at a mode of information processing at the cellular level. In the microchips that run our computers, information processing capabilities reduce data to unambiguous zeros and ones. In cells, it’s not that simple. DNA, proteins, lipids and sugars are arranged in complex and compartmentalized structures.

But scientists — who want to harness the potential of cells as living computers that can respond to disease, efficiently produce biofuels or develop plant-based chemicals — don’t want to wait for evolution to craft their desired cellular system.

In a published May 25 in , a team of 91Ě˝»¨synthetic biology researchers have demonstrated a new method for digital information processing in living cells, analogous to the logic gates used in electric circuits. They built a set of synthetic genes that function in cells like , commonly used in electronics, which each take two inputs and only pass on a positive signal if both inputs are negative. NOR gates are functionally complete, meaning one can assemble them in different arrangements to make any kind of information processing circuit.

The 91Ě˝»¨engineers did all this using DNA instead of silicon and solder, and inside yeast cells instead of at an electronics workbench. The circuits the researchers built are the largest ever published to date in eurkaryotic cells, which, like human cells, contain a nucleus and other structures that enable complex behaviors.

Cells could potentially be reprogrammed to undergo new developmental pathways, to regrow organs or to develop entirely new ones. In such developing tissues, cells have to make complex digital decisions about what genes to express and when, and the new technology could be used to control that process.

“While implementing simple programs in cells will never rival the speed or accuracy of computation in silicon, genetic programs can interact with the cell’s environment directly,” said senior author and 91Ě˝»¨electrical engineering professor . “For example, reprogrammed cells in a patient could make targeted, therapeutic decisions in the most relevant tissues, obviating the need for complex diagnostics and broad spectrum approaches to treatment.”

Each cellular NOR gate consists of a gene with three programmable stretches of DNA — two to act as inputs, and one to be the output. The authors then took advantage of a relatively new technology known as to target those specific DNA sequences inside a cell. The Cas9 protein acts like a molecular gatekeeper in the circuit, sitting on the DNA and determining if a particular gate will be active or not.

If a gate is active, it expresses a signal that directs the Cas9 to deactivate another gate within the circuit. In this way, the researchers can “wire” together the gates to create logical programs in the cell.

What sets the study apart from previous work, researchers said, is the scale and complexity of the circuits successfully assembled — which included up to seven NOR gates assembled in series or parallel.

At this size, circuits can begin to execute really useful behaviors by taking in information from different environmental sensors and performing calculations to decide on the correct response. Imagined applications include engineered immune cells that can sense and respond to cancer markers or cellular biosensors that can easily diagnose infectious disease in patient tissue.

These large DNA circuits inside cells are a major step toward an ability to program living cells, the researchers said. They provide a framework where logical programs can be easily implemented to control cellular function and state.

The research was funded by the Semiconductor Research Corporation and the National Science Foundation.

Co-authors include 91Ě˝»¨electrical engineering graduate student , bioengineering graduate student , chemical engineering graduate student and chemical engineering professor .

For more information, contact Eric Klavins at klavins@uw.edu.

For centuries, humans have been playing with yeast. But these simple fungal cells usually do their jobs — making bread rise or converting sugar into alcohol — without having to communicate or work together.

Now, a team of 91Ě˝»¨ researchers has engineered yeast cells () that can “talk” to one another, using a versatile plant hormone called auxin. In a June 23 in the American Chemical Society’s journal , the researchers describe a novel cell-to-cell communication system that enables one yeast cell to regulate the expression of genes and influence the behavior of an entirely separate yeast cell.

It’s a basic step in understanding the communication and cooperative processes that might lead to synthetic stem cells that could grow into artificial organs or organisms that require different types of cells to work together.

“Until you can actually build a multicellular organism that starts from a single cell, you don’t really understand it. And until we can do that, it’s going to be hard to do things like regrow a kidney for someone who needs it,” said senior author , a 91Ě˝»¨associate professor of electrical engineering and of bioengineering.

It might also enable engineered yeast to perform complicated behaviors that coordinated multicellular systems such as our immune system can pull off, like recognizing an invading pathogen and mounting a response. If so, one might program those cells to collaboratively diagnose the flu or malaria: just add saliva to a packet of yeast and see if it changes color.

For now, though, the team spearheaded by lead authors , a 91Ě˝»¨doctoral student in bioengineering, and , a 91Ě˝»¨doctoral student in electrical engineering, simply wanted to see if it could induce one yeast cell to send a signal that sets off a cascade of changes in another cell.

In the initial experiment, they used the plant hormone auxin — which yeast cells don’t normally recognize or respond to — to “turn off” a target gene in another cell. In this case, the gene that was switched off was an inserted jellyfish gene that turned the yeast fluorescent green.

“This project was to find out whether we could use auxin to make the cells talk to each other in a really simple way,” said Klavins. “We’re not sending complicated messages yet. One cell is saying ‘hello?’ and the other cell says ‘I can hear you.’ Eventually they’ll say ‘I’m this kind of cell. What are you? Let’s work together.’ But for now it’s pretty much ‘hi.'”

Synthetic biologists, who assemble genetic parts in new ways with the goal of popping them into an organism to produce reliable behaviors, have struggled to build modules that enable cell-to-cell communication in organisms that don’t naturally do it.

The 91Ě˝»¨team overcame this hurdle by engineering a suite of novel — proteins that control whether a specific gene inside a cell’s DNA is expressed or not — with varying sensitivities to auxin. That “tunability” offers important control in regulating cell behavior.

With co-author and 91Ě˝»¨associate biology professor , the 91Ě˝»¨team figured out how to make a “sender” yeast cell produce auxin, a versatile hormone that controls everything from where a plant’s roots develop to how effectively they fight off pathogens. Through trial and error, the team learned an enzyme borrowed from a soil bacterium can induce yeast to convert a commonly available chemical into auxin.

In the “receiver” yeast cells, the researchers inserted the new transcription factor — which was assembled from so many different genetic parts that they call it the “Frankenfactor” – and engineered it to activate the jellyfish gene that turned the cell green.

When the sender cell released auxin, additional proteins that the researchers introduced in the receiver cell were able to degrade the Frankenfactor and switch off the gene that turned the receiver cell green.

That type of simple communication forms the bedrock of multicellular organisms in which different types of cells collaborate to carry out complicated tasks. As a next step, the 91Ě˝»¨team plans to test whether auxin can induce more complex behaviors in yeast cells, such as forming patterns or cooperatively computing basic functions.

Since auxin is a plant hormone, mammalian cells also ignore it, making auxin a potentially useful tool in designing gene therapies or other applications without adverse reactions in humans. The 91Ě˝»¨method, which uses a “guide RNA” to target the gene of interest, could be adapted to produce a number of genetic or behavior changes.

“If you ask someone in computer science what they can do with a programming language, they’ll laugh and say they can do anything with it,” Klavins said. “If we can figure out the programming language of life, we can do anything that life does — except in a more controllable, reliable way.”

The research was funded by the National Science Foundation and the Paul Allen Family Foundation.

For more information, contact Klavins at klavins@u.washington.edu.

NSF grant numbers: 1411949, 1137266 (EFRI-MKS), 1317653